6GXX | pdb_00006gxx

Fab fragment of an antibody selective for alpha-1-antitrypsin in the native conformation

• PDB DOI: https://doi.org/10.2210/pdb6GXX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2018-06-27 Released: 2019-07-10 
• Deposition Author(s): Elliston, E.L.K., Miranda, E., Perez, J., Lomas, D.A., Irving, J.A.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust, Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Characterisation of a monoclonal antibody conformationally-selective for native alpha-1-antitrypsin

Elliston, E.L.K., Miranda, E., Perez, J., Irving, J.A., Lomas, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis, gel filtration

Macromolecule Content 

• Total Structure Weight: 48.04 kDa 
• Atom Count: 3,880 
• Modeled Residue Count: 435 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB 1D9 heavy chain	A [auth H]	226	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB 1D9 light chain	B [auth L]	217	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.103	α = 90
b = 85.257	β = 90
c = 89.427	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Elliston, E.L.K., Miranda, E., Perez, J., Lomas, D.A., Irving, J.A.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/N024842/1
Wellcome Trust	United Kingdom	Wellcome Trust 4-year PhD Interdisciplinary Programme in Structural, Computational and Chemical Biology
Other private	United States	Alpha-1 Foundation project grant to James Irving
Other private	United States	Alpha-1 Foundation pilot grant to Elena Miranda
Other government	United Kingdom	UCLH/NIHR Biomedical Research Centre

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary